def test_blast(tmpdir):
a = asm.Assembly([('aardvark',
asm.aflist(
0,
''.join([
'tcatatctggcgttaatggagttcagtggtaatacaatgaccag',
'agatgcatccagagcagttctgcgttttgtcactgtcacagcag',
'aagccttacgcttcaggcagat'
]),
'-',
trackclass='nucleotide')),
('b',
asm.aflist(
2, 'GGATCCATC', '-', trackclass='nucleotide')),
('c', asm.aflist(0, 'AAA', '-',
trackclass='nucleotide'))])
a.serialize(str(tmpdir.join('asm.json.bz2')))
class Args:
assembly = str(tmpdir.join('asm.json.bz2'))
label = 'aardvark'
json = 'data/blast_subcommand.json'
xml = 'data/blast_subcommand.xml'
n = 10
assert seqlab.subcommands.blast.action(Args()) == 0
assert os.path.exists('data/blast_subcommand.json')
assert os.path.exists('data/blast_subcommand.xml')
with open('data/blast_subcommand.json') as h:
j = json.load(h)
assert len(j) <= 10
def test_render(tmpdir):
a = asm.Assembly([('a', asm.aflist(0, 'ATGGNTGG-TC', '-', trackclass='nucleotide')),
('b', asm.aflist(2, 'GGATCCATC', '-', trackclass='nucleotide')),
('c', asm.aflist(0, 'AAA', '-', trackclass='nucleotide'))])
a.serialize(str(tmpdir.join('asm.json.bz2')))
class Args:
assembly = str(tmpdir.join('asm.json.bz2'))
output = 'data/render_subcommand_test.html'
assert seqlab.subcommands.render.action(Args()) == 0
assert os.path.exists('data/render_subcommand_test.html')
def test_statistics(tmpdir):
a = asm.Assembly([('a', asm.aflist(0, 'ATGGNTGG-TC', '-')),
('b', asm.aflist(2, 'GGATCCATC', '-')),
('c', asm.aflist(0, 'AAA', '-'))])
a.serialize(str(tmpdir.join('asm.json.bz2')))
class Args:
assembly = str(tmpdir.join('asm.json.bz2'))
label1 = 'a'
label2 = 'b'
fields = ','.join(['identities','mismatches','fracoverlap'])
output = str(tmpdir.join('test.csv'))
assert seqlab.subcommands.statistics.action(Args()) == 0
with open(str(tmpdir.join('test.csv'))) as h:
cr = csv.reader(h)
assert cr.next() == ['5','3','0.9']
def test_addsequences(tmpdir):
a = asm.Assembly([('a', asm.aflist(0, 'ATGATGGA', '-'))])
a.serialize(str(tmpdir.join('asm.json.bz2')))
with open(str(tmpdir.join('a.fasta')), 'w') as h:
print >>h, '>alpha omega\nTGATGGA\n'
class Args:
assembly=str(tmpdir.join('asm.json.bz2'))
output=str(tmpdir.join('output.json.bz2'))
align_to='a'
fastas=[str(tmpdir.join('a.fasta'))]
no_alignment=False
assert seqlab.subcommands.addsequence.action(Args()) == 0
assert os.path.exists(str(tmpdir.join('output.json.bz2')))
asm2 = asm.deserialize(str(tmpdir.join('output.json.bz2')))
assert asm2 == asm.Assembly([('a', asm.aflist(0, 'ATGATGGA', '-')),
('alpha omega', asm.aflist(1, 'TGATGGA', '-'))])
def test_blast(tmpdir):
a = asm.Assembly([('aardvark',
asm.aflist(0,
''.join(['tcatatctggcgttaatggagttcagtggtaatacaatgaccag',
'agatgcatccagagcagttctgcgttttgtcactgtcacagcag',
'aagccttacgcttcaggcagat']),
'-',
trackclass='nucleotide')),
('b', asm.aflist(2, 'GGATCCATC', '-', trackclass='nucleotide')),
('c', asm.aflist(0, 'AAA', '-', trackclass='nucleotide'))])
a.serialize(str(tmpdir.join('asm.json.bz2')))
class Args:
assembly = str(tmpdir.join('asm.json.bz2'))
label = 'aardvark'
json = 'data/blast_subcommand.json'
xml = 'data/blast_subcommand.xml'
n = 10
assert seqlab.subcommands.blast.action(Args()) == 0
assert os.path.exists('data/blast_subcommand.json')
assert os.path.exists('data/blast_subcommand.xml')
with open('data/blast_subcommand.json') as h:
j = json.load(h)
assert len(j) <= 10